The RNA Response to DNA Damage

The RNA response to DNA damage Luciana E. Giono, Nicola´s Nieto Moreno, Adriań E. Cambindo Botto, Gwendal Dujardin, Manuel J. Munõz, Alberto R. Kornblihtt PII: DOI: Reference: S0022-2836(16)00177-7 doi: <a href="/goto?url=http://dx.doi.org/10.1016/j.jmb.2016.03.004" target="_blank">10.1016/j.jmb.2016.03.004 </a>YJMBI 65022 To appear in: Journal of Molecular Biology Received date: Revised date: Accepted date: 10 December 2015 1 March 2016 7 March 2016 Please cite this article as: Giono, L.E., Moreno, N.N., Botto, A.E.C., Dujardin, G., Munõz, M.J. & Kornblihtt, A.R., The RNA response to DNA damage, Journal of Molec- ular Biology (2016), doi: <a href="/goto?url=http://dx.doi.org/10.1016/j.jmb.2016.03.004" target="_blank">10.1016/j.jmb.2016.03.004 </a>This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. ACCEPTED MANUSCRIPT The RNA response to DNA damage Luciana E. Giono1, Nicolás Nieto Moreno1, Adrián E. Cambindo Botto1, Gwendal Dujardin1,2, Manuel J. Muñoz1, and Alberto R. Kornblihtt1* 1Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina 2Centre for Genomic Regulation. Dr. Aiguader 88, E-08003 Barcelona, Spain. * Corresponding author: [email protected] ACCEPTED MANUSCRIPT Abstract Multicellular organisms must ensure genome integrity to prevent accumulation of mutations, cell death, and cancer. The DNA damage response (DDR) is a complex network that senses, signals and executes multiple programs including DNA repair, cell cycle arrest, senescence and apoptosis. This entails regulation of a variety of cellular processes: DNA replication and transcription, RNA processing, mRNA translation and turnover, and post-translational modification, degradation and relocalization of proteins. Accumulated evidence over the past decades has shown that RNAs and RNA metabolism are both regulators and regulated actors of the DDR. This review aims to present a comprehensive overview of the current knowledge on the many interactions between the DNA damage and RNA fields. Research highlights: • The DNA damage response is essential for genome integrity in multicellular organisms. • RNAs and RNA metabolism play a prominent role in the DNA damage response (DDR). • Splicing factors and RNA binding proteins are regulators of and regulated by the DDR. • Small and long non coding RNAs and miRNAs also participate in the DDR. ACCEPTED MANUSCRIPT Key words: DNA damage response; p53; RNA processing; alternative splicing; ncRNAs Abbreviations ARE: AU-rich sequence elements ARE-BP: ARE-binding protein AS: Alternative splicing BER: Base excision repair CPT: Camptothecin CS: Cockayne syndrome CTD: C-terminal domain DOX: Doxorubicin (Adriamycin) DDR: DNA damage response DDRNAs: DNA damage response RNAs DSB: DNA double-strand break ETO: Etoposide GGR: Global genome repair hnRNP: heterogeneous nuclear ribonucleoprotein IR: Ionizing radiation lincRNAs: Long intergenic non coding RNAs NMD: Nonsense mediated decay RNAi: RNA interference ACCEPTED MANUSCRIPT RNAPII: RNA polymerase II TCR: Transcription-coupled repair miRNA: microRNA ncRNA: non-protein-coding RNA NER: Nucleotide excision repair RBP: RNA binding protein SR proteins: serine-arginine proteins UVsS: UV-sensitive syndrome XP: Xeroderma pigmentosum 1. The expanding universe of RNAs Scientific breakthroughs often follow technical breakthroughs. Forty years ago, the isolation and application of restriction enzymes, the development RNA-DNA hybridization methods combined with electron microscopy and the Southern blot technique were among the tools that led to a “mini-revolution in molecular genetics” [1]: the discovery of split genes and RNA splicing that resulted in the 1993 Nobel Prize to Philip Sharp and Richard Roberts. In the following years, a handful of genes giving rise to different mRNA variants through alternative splicing were described and thought to be rare, exceptional events. We know today that, in humans, about 95% of genes display alternative splicing, multiplying the functional diversity of the mRNAs - and proteins- generated [2]. Alternative splicing can be both cause and result of natural ACCEPTED MANUSCRIPT and pathological cellular processes as diverse as cell proliferation and differentiation, cancer, cystic fibrosis, hemophilia, and spinal muscle atrophy, among many others [3]. In the past two decades, the development of RNA sequencing and other highthroughput-sequencing technologies, coupled with powerful computational analysis, has opened our eyes to an expanding universe of non-protein-coding RNAs (ncRNAs) [4]. These RNAs function in regulatory mechanisms affecting virtually every single cellular process. In the past few years, mounting evidence has shown an important role in the DDR of proteins involved in RNA metabolism. Moreover, recently identified ncRNAs termed diRNAs [DNA double-strand break (DSB-induced RNAs] and DDRNAs (DNA damage response RNAs) are generated at sites of damage, modulate the DDR, and promote DNA repair [5, 6]. This review will focus on how RNAs are regulated and, in turn, regulate the cellular response to DNA damage, with emphasis on alternative splicing. 2. The cellular DNA damage response Maintenance of genome stability is an absolute requirement for cell survival and stable propagation of genetic information. Yet cells are constantly challenged by the generation of close to 105 spontaneous DNA lesions per cell on a daily basis, resulting from hydrolytic reactions, and reactive oxygen and nitrogen species and other metabolic products. DNA is also damaged by exogenous agents such as ionizing radiation (IR) and UV light and, for instance, sunlight exposure can increase that number by up to 105 additional lesions [7, 8]. ACCEPTED MANUSCRIPT To deal with this constant assault, cells have evolved an intricate signaling network - collectively referred to as the DDR- that activates cell cycle checkpoints and DNA repair pathways, and regulates different aspects of cell biology such as DNA replication, transcription, recombination, chromatin remodeling, and differentiation. Ultimately, this signaling network will determine the outcome: DNA repair and cell survival, replicative senescence, or apoptosis [8]. Premature ageing, cancer predisposition, and an overwhelming list of human diseases associated with defects in the DDR highlight its vital significance [9]. Specific lesions or categories of lesions are detected by at least five independent sensor complexes that activate specialized signaling and DNA repair pathways. Central to the DDR are the transducers ATM, ATR, and DNA-PK, of the PI3K-like family of protein kinases, and the poly(ADP-ribose) polymerase members PARP1 and PARP2, which are recruited to sites of DNA damage, leading to the formation of large nuclear foci termed “DDR foci” [10-12]. There, post-translational modification of downstream substrates and extensive chromatin remodeling play prominent roles [13]. Most of the current knowledge about the DDR is centered on ATM and ATR and their downstream targets, the mediator kinases Chk1 and Chk2, and the more recently described p38MAPK and MK2, which activate numerous effector proteins [10]. Either ATM, ATR, or the downstream mediator kinases can phosphorylate the tumor suppressor p53, one of the most important and best characterized effectors of the DDR. p53 is tightly regulated in unstressed cells and becomes stabilized and activated through multiple posttranslational modifications upon DNA damage and other types of stress [14]. ACCEPTED MANUSCRIPT Integrating signals from many different pathways, p53 regulates the expression of an extensive list of targets genes involved in numerous cellular processes of the DDR: cell cycle progression, DNA repair, senescence, apoptosis, metabolism, and angiogenesis, among others [15]. The outcome of the DDR appears to be stimuli- and cell-type specific and the rules governing this life-or-death decision still remain elusive [16]. The DDR can be viewed as a two-step process: a first and fast initiation response is mediated by post-translational modifications, regulating activity, localization, stability and protein-protein interactions of numerous substrates [13]. A second -and necessarily slower- maintenance response involves newly synthesized mRNAs that can be regulated at the level of transcription, splicing, and 5’- and 3’-end processing. In between, pre-existing mRNAs can be post-transcriptionally regulated through modulation of their stability and translation, allowing cells a rapid adjustment [17]. As will be discussed in the following sections, the RNA response to DNA damage is affected by both post-translational modifications and the elicited transcriptional programs. 3. Transcription and mRNA processing during the DDR 3a. RNA polymerase II In eukaryotes, all mRNAs and many ncRNAs are transcribed by RNA polymerase II (RNAPII), a holoenzyme composed of 12 subunits. Rpb1, the largest and catalytic subunit, contains an evolutionarily conserved C-terminal domain (CTD) composed, in mammalian cells, of 52 tandem repeats of a heptad (YSPTSPS) containing five phospho- ACCEPTED MANUSCRIPT acceptor residues. In normal cells, the CTD undergoes cycles of phosphorylation/dephosphorylation and plays critical roles during the cycle of transcription initiation, elongation, and termination, and in many other aspects of RNA processing [18]. In cells that have sustained DNA damage, the RNAPII and its CTD are also critical for sensing the damage and contribute to organizing the DDR [19, 20]. For many years it has been known that some DNA lesions constitute a potent block to transcription by elongating RNAPII. This is particularly the case for the bulky UV- induced DNA lesions. Because transcription blocks may disturb cellular homeostasis with potentially fatal outcome, cells have evolved a dedicated repair pathway: transcription-coupled repair (TCR), a subpathway of nucleotide excision repair (NER) [21]. Different models have been proposed as to how cells deal with the stalled RNAPII, the common denominator being that the polymerase must be displaced in order to allow access of repair factors to the lesion. Within minutes of treating cells with UV light, cisplatin (CIS) or camptothecin (CPT), all agents that generate DNA lesions that are repaired by NER, a fraction of Rpb1 becomes hyperphosphorylated, ubiquitinated and degraded by the proteasome [22, 23]. Alternatively, RNAPII may reverse translocate (backtracking) or, less frequently, bypass the lesion, with the possibility of transcriptional mutagenesis [24]. More recent studies indicate that RNAPII degradation occurs only as “a last resort”, favoring the backtracking model [25]. In either case, all three scenarios require the assistance of TCR specific factors that are recruited to the chromatin by the arrested RNAPII, mainly CSA, CSB, UVSSA, XAB2, HMGN1 [21]. Following the initial recognition, the core NER proteins, common to the global genome ACCEPTED MANUSCRIPT repair (GGR) NER subpathway, are then recruited and the lesion is removed (for a review on NER see ref. [26]). The importance and complexity of the NER pathways is underscored by hereditary diseases of varied phenotypes and severity associated to mutations of the involved factors observed in patients with Cockayne and UV-sensitive syndromes (CS and UVsS, TCR-deficient), and Xeroderma pigmentosum (XP, GGR- or GGR/TCR-deficient) [27]. The half-life of RNAPII arrested at a UV-induced cyclobutane pyrimidine dimer (CPD) is ~ 20 hours in vitro, making RNAPII the most sensitive damage detector “by proxy” known to date. Moreover, the recent realization of the extent of pervasive transcription gives RNAPII and TCR a significantly more important role in DNA repair than previously acknowledged [28]. In addition to initiating TCR, and no less importantly, stalled RNAPII has been reported to trigger the activation of DNA damage checkpoints, causing phosphorylation and accumulation of p53 in an RPA- and ATM/ATR- dependent manner [19]. As mentioned above, treatment with UV light or CPT induces hyperphosphorylation of RNAPII and the positive transcription elongation factor b (P-TEFb) has been implicated in this modification. P-TEFb, composed of cyclin-dependent kinase 9 (Cdk9) and a regulatory cyclin T subunit, is found in cells in two different forms: an active kinase, P- TEFb small complex, or an inactive large complex composed of P-TEFb, the snRNA 7SK, two HEXIM subunits, LARP7, and MePCE [29]. UV, CPT, and other stimuli have been reported to release P-TEFb from the 7SK snRNP complex, and this is concurrent ACCEPTED MANUSCRIPT with RNAPII hyperphosphorylation by Cdk9, reduced elongation, and transcriptional repression [30]. Despite the similarities, pre-treatment of cells with caffeine, a broad inhibitor of the PI3K family of kinases, prevented P-TEFb release following UV but not CPT. The implications of this observation remain unclear, as specific inhibitors of the DDR kinases ATR, ATM and DNA-PK had no effect on P-TEFb release or transcription inhibition. This observation suggests the involvement of another signaling protein and different signaling pathways activated by UV and CPT [31]. Hexamethylene bisacetamide (HMBA), a differentiation inducing agent, was also shown to release P- TEFb from the 7SK snRNP complex and this was accompanied by p53 activation, p21 induction, and cell cycle arrest. p53 was co-immunoprecipitated with Cdk9 and cyclin T, but not HEXIM, suggesting its association with the catalytic active P-TEFb complex. This interaction was proposed to allow p53 to recruit P-TEFb to the p21 gene [32]. In yeast, interfering with the binding of a number of phospho CTD-associating proteins (PCAPs), or inducing aberrant phosphorylation of RNAPII’s CTD, led to increased DNA damage sensitivity. Based on these results, a CTD-associated DNA damage response (CAR) system was proposed, that is composed of PCAPs and organized around the phospho CTD of elongating RNAPII. Most of the components of the CAR system are evolutionarily conserved and although an equivalent role in humans awaits confirmation, some of these proteins had already been linked to cancer [20]. 3b. Gene transcription ACCEPTED MANUSCRIPT Damaged DNA poses a threat to transcription: RNAPII may stall at lesions or bypass them, with the potential risk of transcriptional mutagenesis. Preventing this, UV irradiation and other types of DNA damage have been shown to transiently inhibit the synthesis and processing of mRNAs. Although it has been reported that the repression of RNA synthesis by DNA damage is a global phenomenom [33, 34], some studies suggest that it might be in fact a local effect [35-38]. Regardless, cells rely heavily on gene transcription to mount an appropriate DDR and ensure checkpoint maintenance and genome stability. The best example of this is the DNA damage transcriptional response mediated by p53 [39], but other transcription factors contribute also to the DDR. In cells that have sustained a limited amount of damage, NF-B activation would regulate cell survival pathways, tipping the balance towards cell cycle arrest and DNA repair rather than apoptosis [40]. This requirement for transcription amid transcription inhibition represents a paradox, and the transcription-coupled DNA repair pathway is only one of the mechanisms that cells have evolved in order to face this situation. Failure to recover from transcription inhibition following UV irradiation is one of the hallmarks of TCR-deficient CS cells. However, evidence suggests that this is not solely due to impaired DNA repair of actively transcribed genes, and that in addition to the physical block imposed by lesions, other mechanisms are set in place that inhibit transcription [33, 41]. One study addressed this transcription paradox while providing an original perspective on p53 life-or-death decisions. An analysis of p53-induced genes following UV irradiation showed that increasing the dose of UV light caused a decrease in the number ACCEPTED MANUSCRIPT of transcribed genes but also a shift towards the transcription of more compact genes, with fewer and smaller introns. Interestingly, these compact genes were enriched for initiators of apoptosis. This is consistent with the fact that the probability of transcription blocking by DNA lesions depends on the amount of lesions and the size of the transcribed genes and suggests a passive mechanism that would promote apoptosis in cells that have sustained levels of DNA damage beyond repair [42]. More recently, the general transcription factor TFIIB was revealed as a key element allowing a general attenuation of cellular transcription while leaving the p53 transcriptional response intact. TFIIB is an essential component of the RNAPII preinitiation complex but also plays a role in transcription termination through interactions with the 3’-end processing factors CPSF and CstF-64 in a phosphorylation-dependent manner. Although modification of TFIIB and, consequently, gene transcription, is reduced upon DNA damage, p53 was shown to directly interact with CstF, providing an alternative mechanism for the recruitment of termination factors to p53 target genes [43]. In line with this observation, some p53 target genes were reported to have different requirements regarding transcription. As mentioned above, P-TEFb activation by HMBA was shown to induce the prototypical p53 target gene p21 [32]. However, although P-TEFb activity appears to be sufficient for p21 induction, it also appears to be dispensable for activation in certain contexts. Indeed, and unlike most genes, p21 did not require P-TEFb kinase activity, phosphorylation of RNAPII at serine 2 nor recruitment of the elongation factor FACT. Moreover, pharmacological inhibition of P- ACCEPTED MANUSCRIPT TEFb Cdk9 that led to global transcription inhibition resulted in p53 accumulation and activation, p53 target gene induction, and p53-dependent apoptosis [44]. 3c. Post-transcriptional regulation With transcription inhibition, the regulation of the pool of preexisting transcripts becomes a key controlling point during the DDR. Reports have shown that mRNAs can be regulated at the level of maturation, nuclear export, stability and translational activity. With the exception of histone mRNAs, all eukaryotic mRNAs undergo 3’ end endonucleolytic cleavage followed by addition of some 200 adenosine residues, the poly(A) tail. 3’-end formation and 3’ processing factors have been shown to play a significant role in the DDR through the global and gene-specific regulation of the synthesis and stability of mRNAs [45]. Upon UV irradiation, two proteins involved in DNA repair and checkpoint activation, BRCA1 and BARD1, regulate 3’-end formation. BRCA1 and an ATM-phosphorylated BARD1 form a complex that binds to CstF-50 and inhibits mRNA 3’-end cleavage and polyadenylation [46]. Similarly, p53 negatively regulates 3’ processing through binding to the CstF/BARD1 complex [47]. THOC5 is a member of the TREX (transcription/export) family and a component of the THO complex that is recruited to protein coding genes, coupling transcription with mRNA export. Upon DNA damage, p53- and ATM-dependent phosphorylation of ACCEPTED MANUSCRIPT THOC5 impaired its ability to bind mRNA, causing a drastic reduction in the cytoplasmic pool of a set of THOC5-dependent mRNAs. Of note, p53 effectors and regulators were among the THOC5-independent mRNAs whose export remained unaffected [48]. Microarray analysis of polysome-bound vs. total RNA showed that, both in human astrocytes and brain tumor cells, IR affects gene expression primarily at the level of translation: 10 times more genes were found regulated through their recruitment to and away from polysomes compared to those modulated through transcription. Interestingly, a considerable fraction of these genes were involved in transcription regulation and RNA metabolism [49]. In human breast cells, IR causes an early and transient increase in translation through an ATM-, ERK-, and mTOR-dependent but p53-independent inhibitory phosphorylation of the 4E-BP1 factor. Following this initial wave, 4E-BP1 shifts to the hypophosphorylated form, becomes stabilized and, by associating with eIF4E, inhibits protein synthesis [50]. Finally, in mouse embryonic stem cells, CIS treatment led to mRNA translation arrest, protecting cells from genotoxic stress [51]. In addition to these global regulatory mechanisms, the DDR can also affect the stability and translation of specific mRNAs through the association of RNA binding proteins (RBPs) to sequence elements that are frequently, but not exclusively, found in the 3’UTRs of mRNAs. Different classes of AU-rich sequence elements (AREs) have been described that regulate mRNA stability and translation. The recognition of theses motifs by ARE-binding proteins (ARE-BPs) is promiscuous: the same ARE can bind different ACCEPTED MANUSCRIPT ARE-BPs and many ARE-BPs have been shown to interact with multiple ARE- containing mRNAs. This sets a scenario for cooperative and antagonistic behaviors between ARE-BPs towards a given mRNA [52]. In many cases, these ARE-containing mRNAs encode effectors of the DDR and allow cells a rapid response [53, 54]. The first observation linking the DDR with RBPs was reported over two decades ago when UV and other DNA damaging agents were shown to upregulate and/or activate up to 13 RBPs [55]. Subsequently, transcripts from the five growth arrest and DNA damage-inducible (GADD) genes, all of which contain ARE elements in their 3’UTR, were found to become stabilized following DNA damage [56]. In particular, GADD45 is a p53 target gene that contributes to G2/M cell cycle arrest, apoptosis, and DNA repair [57]. In unstressed cells, GADD45 expression is negatively regulated by a dual mechanism involving AREs present in the mRNA 3’UTR: 1) binding of the ARE-BP AUF1 promotes its decay, and 2) binding of the TIA1-related protein TIAR suppresses its translation [58]. Upon genotoxic stress, the association of AUF1 and p38-phosphorylated TIAR to GADD45 mRNA is dramatically reduced. Conversely, MK2 phosphorylation of hnRNPA0 stimulates its binding to the GADD45 3’UTR, stabilizing the mRNA [59]. In addition to AREs, TIAR can bind to C-rich motifs that, when inserted into heterologous reporters, were able to suppress their translation. Treatment of cells with UV caused several mRNAs to dissociate from TIAR, upregulating the levels of the encoded proteins that included effectors/modulators of the DDR like Apaf-1 and TCF3 [60], and translation factors PABPN1, ETF1, TUFM, EIF5a, and RPL24 [61].

The RNA Response to DNA Damage

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